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Leuzzi G, Vasciaveo A, Taglialatela A, Chen X, Firestone TM, Hickman AR, Mao W, Thakar T, Vaitsiankova A, Huang JW, Cuella-Martin R, Hayward SB, Kesner JS, Ghasemzadeh A, Nambiar TS, Ho P, Rialdi A, Hebrard M, Li Y, Gao J, Gopinath S, Adeleke OA, Venters BJ, Drake CG, Baer R, Izar B, Guccione E, Keogh MC, Guerois R, Sun L, Lu C, Califano A, Ciccia A. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell 2024; 187:861-881.e32. [PMID: 38301646 PMCID: PMC10980358 DOI: 10.1016/j.cell.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/23/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.
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Affiliation(s)
- Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Vasciaveo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | | | - Wendy Mao
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanay Thakar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alina Vaitsiankova
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jordan S Kesner
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ali Ghasemzadeh
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander Rialdi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxime Hebrard
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jinmei Gao
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | | | - Charles G Drake
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lu Sun
- EpiCypher Inc., Durham, NC 27709, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LÁ, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin A, Savojardo C, Martelli PL, Casadio R, Tubiana J, Wolfson H, Oliva R, Barradas-Bautista D, Ricciardelli T, Cavallo L, Venclovas Č, Olechnovič K, Guerois R, Andreani J, Martin J, Wang X, Kihara D, Marchand A, Correia B, Zou X, Dey S, Dunbrack R, Levy E, Wodak S. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics 2023; 23:e2200323. [PMID: 37365936 PMCID: PMC10937251 DOI: 10.1002/pmic.202200323] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/28/2023]
Abstract
Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Julia K. Varga
- Hebrew University of Jerusalem Institute for Medical Research Israel-Canada
| | | | | | | | | | | | | | - Jérôme Tubiana
- Tel Aviv University Blavatnik School of Computer Science
| | - Haim Wolfson
- Tel Aviv University Blavatnik School of Computer Science
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Institute for Data Science and Informatics, University of Missouri
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3
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Singh DK, Gamboa RS, Singh AK, Walkemeier B, Van Leene J, De Jaeger G, Siddiqi I, Guerois R, Crismani W, Mercier R. The FANCC-FANCE-FANCF complex is evolutionarily conserved and regulates meiotic recombination. Nucleic Acids Res 2023; 51:2516-2528. [PMID: 36652992 PMCID: PMC10085685 DOI: 10.1093/nar/gkac1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/29/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023] Open
Abstract
At meiosis, programmed meiotic DNA double-strand breaks are repaired via homologous recombination, resulting in crossovers (COs). From a large excess of DNA double-strand breaks that are formed, only a small proportion gets converted into COs because of active mechanisms that restrict CO formation. The Fanconi anemia (FA) complex proteins AtFANCM, MHF1 and MHF2 were previously identified in a genetic screen as anti-CO factors that function during meiosis in Arabidopsis thaliana. Here, pursuing the same screen, we identify FANCC as a new anti-CO gene. FANCC was previously only identified in mammals because of low primary sequence conservation. We show that FANCC, and its physical interaction with FANCE-FANCF, is conserved from vertebrates to plants. Further, we show that FANCC, together with its subcomplex partners FANCE and FANCF, regulates meiotic recombination. Mutations of any of these three genes partially rescues CO-defective mutants, which is particularly marked in female meiosis. Functional loss of FANCC, FANCE, or FANCF results in synthetic meiotic catastrophe with the pro-CO factor MUS81. This work reveals that FANCC is conserved outside mammals and has an anti-CO role during meiosis together with FANCE and FANCF.
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Affiliation(s)
- Dipesh Kumar Singh
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Rigel Salinas Gamboa
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Avinash Kumar Singh
- CSIR-Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Imran Siddiqi
- CSIR-Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Wayne Crismani
- The DNA Repair and Recombination Laboratory, St Vincent's Institute of Medical Research, Melbourne 3065, Australia.,The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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4
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Zönnchen J, Gantner J, Lapin D, Barthel K, Eschen-Lippold L, Erickson JL, Villanueva SL, Zantop S, Kretschmer C, Joosten MHAJ, Parker JE, Guerois R, Stuttmann J. EDS1 complexes are not required for PRR responses and execute TNL-ETI from the nucleus in Nicotiana benthamiana. New Phytol 2022; 236:2249-2264. [PMID: 36151929 DOI: 10.1111/nph.18511] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Heterodimeric complexes incorporating the lipase-like proteins EDS1 with PAD4 or SAG101 are central hubs in plant innate immunity. EDS1 functions encompass signal relay from TIR domain-containing intracellular NLR-type immune receptors (TNLs) towards RPW8-type helper NLRs (RNLs) and, in Arabidopsis thaliana, bolstering of signaling and resistance mediated by cell-surface pattern recognition receptors (PRRs). Increasing evidence points to the activation of EDS1 complexes by small molecule binding. We used CRISPR/Cas-generated mutant lines and agroinfiltration-based complementation assays to interrogate functions of EDS1 complexes in Nicotiana benthamiana. We did not detect impaired PRR signaling in N. benthamiana lines deficient in EDS1 complexes or RNLs. Intriguingly, in assays monitoring functions of SlEDS1-NbEDS1 complexes in N. benthamiana, mutations within the SlEDS1 catalytic triad could abolish or enhance TNL immunity. Furthermore, nuclear EDS1 accumulation was sufficient for N. benthamiana TNL (Roq1) immunity. Reinforcing PRR signaling in Arabidopsis might be a derived function of the TNL/EDS1 immune sector. Although Solanaceae EDS1 functionally depends on catalytic triad residues in some contexts, our data do not support binding of a TNL-derived small molecule in the triad environment. Whether and how nuclear EDS1 activity connects to membrane pore-forming RNLs remains unknown.
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Affiliation(s)
- Josua Zönnchen
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
| | - Johannes Gantner
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
| | - Dmitry Lapin
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Department of Biology, Plant-Microbe Interactions, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Karen Barthel
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
| | - Lennart Eschen-Lippold
- Department of Crop Physiology, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
- Department of Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120, Halle, Germany
| | - Jessica L Erickson
- Department of Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120, Halle, Germany
| | - Sergio Landeo Villanueva
- Laboratory of Phytopathology, Wageningen University and Research, 6708 PB, Wageningen, the Netherlands
| | - Stefan Zantop
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
| | - Carola Kretschmer
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University and Research, 6708 PB, Wageningen, the Netherlands
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence in Plant Sciences (CEPLAS), D-40225, Düsseldorf, Germany
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Saclay, F-91198, Gif-sur-Yvette, France
| | - Johannes Stuttmann
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06120, Halle, Germany
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
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5
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Quignot C, Granger P, Chacón P, Guerois R, Andreani J. Atomic-level evolutionary information improves protein-protein interface scoring. Bioinformatics 2021; 37:3175-3181. [PMID: 33901284 DOI: 10.1093/bioinformatics/btab254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/20/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION The crucial role of protein interactions and the difficulty in characterising them experimentally strongly motivates the development of computational approaches for structural prediction. Even when protein-protein docking samples correct models, current scoring functions struggle to discriminate them from incorrect decoys. The previous incorporation of conservation and coevolution information has shown promise for improving protein-protein scoring. Here, we present a novel strategy to integrate atomic-level evolutionary information into different types of scoring functions to improve their docking discrimination. RESULTS : We applied this general strategy to our residue-level statistical potential from InterEvScore and to two atomic-level scores, SOAP-PP and Rosetta interface score (ISC). Including evolutionary information from as few as ten homologous sequences improves the top 10 success rates of individual atomic-level scores SOAP-PP and Rosetta ISC by respectively 6 and 13.5 percentage points, on a large benchmark of 752 docking cases. The best individual homology-enriched score reaches a top 10 success rate of 34.4%. A consensus approach based on the complementarity between different homology-enriched scores further increases the top 10 success rate to 40%. AVAILABILITY All data used for benchmarking and scoring results, as well as a Singularity container of the pipeline, are available at http://biodev.cea.fr/interevol/interevdata/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chloé Quignot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pierre Granger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pablo Chacón
- Department of Biological Chemical Physics, Rocasolano Institute of Physical Chemistry C.S.I.C, Madrid, Spain
| | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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6
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Rahman MM, Mohiuddin M, Shamima Keka I, Yamada K, Tsuda M, Sasanuma H, Andreani J, Guerois R, Borde V, Charbonnier JB, Takeda S. Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination. J Biol Chem 2021; 295:17460-17475. [PMID: 33453991 DOI: 10.1074/jbc.ra120.013521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null MLH3-/- and PMS2-/- mutant cells. We also inserted point mutations into the endonuclease motif of MLH3 and PMS2 genes, generating endonuclease death MLH3DN/DN and PMS2EK/EK cells. MLH3-/- and MLH3DN/DN cells showed a very similar phenotype, a 2.5-fold decrease in the frequency of heteroallelic HR-dependent repair of restriction enzyme-induced double-strand breaks. PMS2-/- and PMS2EK/EK cells showed a phenotype very similar to that of the MLH3 mutants. These data indicate that MLH3 and PMS2 promote HR as an endonuclease. The MLH3DN/DN and PMS2EK/EK mutations had an additive effect on the heteroallelic HR. MLH3DN/DN/PMS2EK/EK cells showed normal kinetics of γ-irradiation-induced Rad51 foci but a significant delay in the resolution of Rad51 foci and a 3-fold decrease in the number of cisplatin-induced sister chromatid exchanges. The ectopic expression of the Gen1 HJ re-solvase partially reversed the defective heteroallelic HR of MLH3DN/DN/PMS2EK/EK cells. Taken together, we propose that MLH3 and PMS2 promote HR as endonucleases, most likely by processing JMs in mammalian somatic cells.
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Affiliation(s)
- Md Maminur Rahman
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mohiuddin Mohiuddin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Islam Shamima Keka
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kousei Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valerie Borde
- Institut Curie, CNRS, UMR3244, PSL Research University, Paris, France
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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7
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Öz R, Wang JL, Guerois R, Goyal G, KK S, Ropars V, Sharma R, Koca F, Charbonnier JB, Modesti M, Strick TR, Westerlund F. Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis. Nucleic Acids Res 2021; 49:2629-2641. [PMID: 33590005 PMCID: PMC7969030 DOI: 10.1093/nar/gkab083] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 01/29/2023] Open
Abstract
We use single-molecule techniques to characterize the dynamics of prokaryotic DNA repair by non-homologous end-joining (NHEJ), a system comprised only of the dimeric Ku and Ligase D (LigD). The Ku homodimer alone forms a ∼2 s synapsis between blunt DNA ends that is increased to ∼18 s upon addition of LigD, in a manner dependent on the C-terminal arms of Ku. The synapsis lifetime increases drastically for 4 nt complementary DNA overhangs, independently of the C-terminal arms of Ku. These observations are in contrast to human Ku, which is unable to bridge either of the two DNA substrates. We also demonstrate that bacterial Ku binds the DNA ends in a cooperative manner for synapsis initiation and remains stably bound at DNA junctions for several hours after ligation is completed, indicating that a system for removal of the proteins is active in vivo. Together these experiments shed light on the dynamics of bacterial NHEJ in DNA end recognition and processing. We speculate on the evolutionary similarities between bacterial and eukaryotic NHEJ and discuss how an increased understanding of bacterial NHEJ can open the door for future antibiotic therapies targeting this mechanism.
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Affiliation(s)
- Robin Öz
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Jing L Wang
- Institut Jacques Monod, Université de Paris, CNRS, UMR7592, Paris, France
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005 France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Rajhans Sharma
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Firat Koca
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille 13009, France
- Equipe Labélisée, Ligue Nationale Contre le Cancer, Paris 75013, France
| | - Terence R Strick
- Institut Jacques Monod, Université de Paris, CNRS, UMR7592, Paris, France
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005 France
- Equipe Labélisée, Ligue Nationale Contre le Cancer, Paris 75013, France
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
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8
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Postic G, Marcoux J, Reys V, Andreani J, Vandenbrouck Y, Bousquet MP, Mouton-Barbosa E, Cianférani S, Burlet-Schiltz O, Guerois R, Labesse G, Tufféry P. Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. J Proteome Res 2020; 19:2807-2820. [PMID: 32338910 DOI: 10.1021/acs.jproteome.0c00066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hierarchical view of the interactions between the members of the flat list becomes highly tedious for large data sets when done by hand. To help hierarchize this data, we introduce a new bioinformatics protocol that integrates information of the multimeric protein 3D structures available in the Protein Data Bank using remote homology detection, as well as information related to Short Linear Motifs and interaction data from the BioGRID. We illustrate on two unrelated use-cases of different complexity how our approach can be useful to decipher the network of interactions hidden in the list of input proteins, and how it provides added value compared to state-of-the-art resources such as Interactome3D or STRING. Particularly, we show the added value of using homology detection to distinguish between orthologs and paralogs, and to distinguish between core obligate and more facultative interactions. We also demonstrate the potential of considering interactions occurring through Short Linear Motifs.
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Affiliation(s)
- Guillaume Postic
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, 75013 Paris, France.,Institut Français de Bioinformatique (IFB), UMS 3601-CNRS, Universite Paris-Saclay, 91400 Orsay, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Victor Reys
- CBS, Univ. Montpellier, CNRS, INSERM, 34095 Montpellier, France
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes, INSERM, CEA, IRIG-BGE, U1038, 38000 Grenoble, France
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Gilles Labesse
- CBS, Univ. Montpellier, CNRS, INSERM, 34095 Montpellier, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, 75013 Paris, France
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9
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Andreani J, Quignot C, Guerois R. Structural prediction of protein interactions and docking using conservation and coevolution. WIREs Comput Mol Sci 2020. [DOI: 10.1002/wcms.1470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jessica Andreani
- Université Paris‐Saclay CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Chloé Quignot
- Université Paris‐Saclay CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Raphael Guerois
- Université Paris‐Saclay CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
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10
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Öz R, Wang J, Guerois R, KK S, Sharma R, Koca F, Modesti M, Strick TR, Westerlund F. Identifying Evolutionarily Conserved Features of NHEJ from Prokaryotes to Eukaryotes using Single-Molecule Approaches. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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11
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Bakail M, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard MC, Courbeyrette R, Mann C, Thuret JY, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du MH, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1. Cell Chem Biol 2019; 26:1573-1585.e10. [PMID: 31543461 DOI: 10.1016/j.chembiol.2019.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/12/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022]
Abstract
Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
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Affiliation(s)
- May Bakail
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Albane Gaubert
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Jessica Andreani
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Gwenaëlle Moal
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Guillaume Pinna
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Ekaterina Boyarchuk
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Marie-Cécile Gaillard
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Regis Courbeyrette
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Carl Mann
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Jean-Yves Thuret
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Bérengère Guichard
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Brice Murciano
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Nicolas Richet
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Adeline Poitou
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Claire Frederic
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Marie-Hélène Le Du
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Morgane Agez
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Caroline Roelants
- Institut National de la Santé et de la Recherche Médicale, Unité 1036, 38000 Grenoble, France; Commissariat à l'Energie Atomique, Institut de Recherche Interdisciplinaire de Grenoble, Biologie du Cancer et de l'Infection, 38000 Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000 Grenoble, France
| | - Zachary A Gurard-Levin
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale, Unité 1036, 38000 Grenoble, France; Commissariat à l'Energie Atomique, Institut de Recherche Interdisciplinaire de Grenoble, Biologie du Cancer et de l'Infection, 38000 Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000 Grenoble, France
| | - Raphael Guerois
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Françoise Ochsenbein
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
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12
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Genera M, Samson D, Raynal B, Haouz A, Baron B, Simenel C, Guerois R, Wolff N, Caillet-Saguy C. Structural and functional characterization of the PDZ domain of the human phosphatase PTPN3 and its interaction with the human papillomavirus E6 oncoprotein. Sci Rep 2019; 9:7438. [PMID: 31092861 PMCID: PMC6520365 DOI: 10.1038/s41598-019-43932-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/27/2019] [Indexed: 02/07/2023] Open
Abstract
The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a PDZ (PSD-95/Dlg/ZO-1) domain-containing phosphatase with a tumor-suppressive or a tumor-promoting role in many cancers. Interestingly, the high-risk genital human papillomavirus (HPV) types 16 and 18 target the PDZ domain of PTPN3. The presence of a PDZ binding motif (PBM) on E6 confers interaction with a number of different cellular PDZ domain-containing proteins and is a marker of high oncogenic potential. Here, we report the molecular basis of interaction between the PDZ domain of PTPN3 and the PBM of the HPV E6 protein. We combined biophysical, NMR and X-ray experiments to investigate the structural and functional properties of the PDZ domain of PTPN3. We showed that the C-terminal sequences from viral proteins encompassing a PBM interact with PTPN3-PDZ with similar affinities to the endogenous PTPN3 ligand MAP kinase p38γ. PBM binding stabilizes the PDZ domain of PTPN3. We solved the X-ray structure of the PDZ domain of PTPN3 in complex with the PBM of the HPV E6 protein. The crystal structure and the NMR chemical shift mapping of the PTPN3-PDZ/peptide complex allowed us to pinpoint the main structural determinants of recognition of the C-terminal sequence of the E6 protein and the long-range perturbations induced upon PBM binding.
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Affiliation(s)
- Mariano Genera
- Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, F-75724, Paris, France.,Sorbonne Université, Complexité du Vivant, F-75005, Paris, France
| | - Damien Samson
- RMN des biomolécules, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie, Institut Pasteur UMR 3528, CNRS, F-75724, Paris, France
| | - Bruno Baron
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Catherine Simenel
- RMN des biomolécules, Institut Pasteur, UMR 3528, CNRS, F-75724, Paris, France
| | - Raphael Guerois
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, Cedex, France
| | - Nicolas Wolff
- Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, F-75724, Paris, France
| | - Célia Caillet-Saguy
- Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, F-75724, Paris, France.
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13
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Visweshwaran SP, Thomason PA, Guerois R, Vacher S, Denisov EV, Tashireva LA, Lomakina ME, Lazennec-Schurdevin C, Lakisic G, Lilla S, Molinie N, Henriot V, Mechulam Y, Alexandrova AY, Cherdyntseva NV, Bièche I, Schmitt E, Insall RH, Gautreau A. The trimeric coiled-coil HSBP1 protein promotes WASH complex assembly at centrosomes. EMBO J 2018; 37:e97706. [PMID: 29844016 PMCID: PMC6028030 DOI: 10.15252/embj.201797706] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/11/2022] Open
Abstract
The Arp2/3 complex generates branched actin networks that exert pushing forces onto different cellular membranes. WASH complexes activate Arp2/3 complexes at the surface of endosomes and thereby fission transport intermediates containing endocytosed receptors, such as α5β1 integrins. How WASH complexes are assembled in the cell is unknown. Here, we identify the small coiled-coil protein HSBP1 as a factor that specifically promotes the assembly of a ternary complex composed of CCDC53, WASH, and FAM21 by dissociating the CCDC53 homotrimeric precursor. HSBP1 operates at the centrosome, which concentrates the building blocks. HSBP1 depletion in human cancer cell lines and in Dictyostelium amoebae phenocopies WASH depletion, suggesting a critical role of the ternary WASH complex for WASH functions. HSBP1 is required for the development of focal adhesions and of cell polarity. These defects impair the migration and invasion of tumor cells. Overexpression of HSBP1 in breast tumors is associated with increased levels of WASH complexes and with poor prognosis for patients.
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Affiliation(s)
- Sai P Visweshwaran
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
| | | | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sophie Vacher
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, Paris, France
| | - Evgeny V Denisov
- Laboratory of Molecular Oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
- Laboratory for Translational Cellular and Molecular Biomedicine, Tomsk State University, Tomsk, Russia
| | - Lubov A Tashireva
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Maria E Lomakina
- Institute of Carcinogenesis, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | | | - Goran Lakisic
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
| | - Sergio Lilla
- Beatson Institute for Cancer Research, Bearsden, UK
| | - Nicolas Molinie
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
| | - Veronique Henriot
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
| | - Yves Mechulam
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
| | | | - Nadezhda V Cherdyntseva
- Laboratory of Molecular Oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Ivan Bièche
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, Paris, France
| | - Emmanuelle Schmitt
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
| | | | - Alexis Gautreau
- Ecole Polytechnique, CNRS UMR7654, Université Paris-Saclay, Palaiseau, France
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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14
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Berto A, Yu J, Morchoisne-Bolhy S, Bertipaglia C, Vallee R, Dumont J, Ochsenbein F, Guerois R, Doye V. Disentangling the molecular determinants for Cenp-F localization to nuclear pores and kinetochores. EMBO Rep 2018; 19:embr.201744742. [PMID: 29632243 DOI: 10.15252/embr.201744742] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 11/09/2022] Open
Abstract
Cenp-F is a multifaceted protein implicated in cancer and developmental pathologies. The Cenp-F C-terminal region contains overlapping binding sites for numerous proteins that contribute to its functions throughout the cell cycle. Here, we focus on the nuclear pore protein Nup133 that interacts with Cenp-F both at nuclear pores in prophase and at kinetochores in mitosis, and on the kinase Bub1, known to contribute to Cenp-F targeting to kinetochores. By combining in silico structural modeling and yeast two-hybrid assays, we generate an interaction model between a conserved helix within the Nup133 β-propeller and a short leucine zipper-containing dimeric segment of Cenp-F. We thereby create mutants affecting the Nup133/Cenp-F interface and show that they prevent Cenp-F localization to the nuclear envelope, but not to kinetochores. Conversely, a point mutation within an adjacent leucine zipper affecting the kinetochore targeting of Cenp-F KT-core domain impairs its interaction with Bub1, but not with Nup133, identifying Bub1 as the direct KT-core binding partner of Cenp-F. Finally, we show that Cenp-E redundantly contributes together with Bub1 to the recruitment of Cenp-F to kinetochores.
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Affiliation(s)
- Alessandro Berto
- Institut Jacques Monod, UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Ecole Doctorale Structure et Dynamique des Systèmes Vivants (#577), Univ Paris Sud, Université Paris-Saclay, Orsay, France
| | - Jinchao Yu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette, France
| | | | - Chiara Bertipaglia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Richard Vallee
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Julien Dumont
- Institut Jacques Monod, UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Francoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette, France
| | - Valérie Doye
- Institut Jacques Monod, UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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15
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Fernandes JB, Duhamel M, Seguéla-Arnaud M, Froger N, Girard C, Choinard S, Solier V, De Winne N, De Jaeger G, Gevaert K, Andrey P, Grelon M, Guerois R, Kumar R, Mercier R. FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination. PLoS Genet 2018; 14:e1007317. [PMID: 29608566 PMCID: PMC5897033 DOI: 10.1371/journal.pgen.1007317] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 04/12/2018] [Accepted: 03/19/2018] [Indexed: 02/07/2023] Open
Abstract
Homologous recombination is central to repair DNA double-strand breaks, either accidently arising in mitotic cells or in a programed manner at meiosis. Crossovers resulting from the repair of meiotic breaks are essential for proper chromosome segregation and increase genetic diversity of the progeny. However, mechanisms regulating crossover formation remain elusive. Here, we identified through genetic and protein-protein interaction screens FIDGETIN-LIKE-1 INTERACTING PROTEIN (FLIP) as a new partner of the previously characterized anti-crossover factor FIDGETIN-LIKE-1 (FIGL1) in Arabidopsis thaliana. We showed that FLIP limits meiotic crossover together with FIGL1. Further, FLIP and FIGL1 form a protein complex conserved from Arabidopsis to human. FIGL1 interacts with the recombinases RAD51 and DMC1, the enzymes that catalyze the DNA strand exchange step of homologous recombination. Arabidopsis flip mutants recapitulate the figl1 phenotype, with enhanced meiotic recombination associated with change in counts of DMC1 and RAD51 foci. Our data thus suggests that FLIP and FIGL1 form a conserved complex that regulates the crucial step of strand invasion in homologous recombination. Homologous recombination is a DNA repair mechanism that is essential to preserve the integrity of genetic information and thus to prevent cancer formation. Homologous recombination is also used during sexual reproduction to generate genetic diversity in the offspring by shuffling parental chromosomes. Here, we identified a novel protein complex (FLIP-FIGL1) that regulates homologous recombination and is conserved from plants to mammals. This suggests the existence of a novel mode of regulation at a central step of homologous recombination.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
- Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Marine Duhamel
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Mathilde Seguéla-Arnaud
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Nicole Froger
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Chloé Girard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Sandrine Choinard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Victor Solier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, CEA-Saclay, Gif-sur-Yvette, France
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
- * E-mail: (RK); (RM)
| | - Raphaël Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
- * E-mail: (RK); (RM)
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16
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Abstract
The structural modeling of protein complexes by docking simulations has been attracting increasing interest with the rise of proteomics and of the number of experimentally identified binary interactions. Structures of unbound partners, either modeled or experimentally determined, can be used as input to sample as extensively as possible all putative binding modes and single out the most plausible ones. At the scoring step, evolutionary information contained in the joint multiple sequence alignments of both partners can provide key insights to recognize correct interfaces. Here, we describe a computational protocol based on the InterEvDock web server to exploit coevolution constraints in protein-protein docking methods. We provide methodology guidelines to prepare the input protein structures and generate improved alignments. We also explain how to extract and use the information returned by the server through the analysis of two representative examples.
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Affiliation(s)
- Aravindan Arun Nadaradjane
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
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17
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Biondini M, Sadou-Dubourgnoux A, Paul-Gilloteaux P, Zago G, Arslanhan MD, Waharte F, Formstecher E, Hertzog M, Yu J, Guerois R, Gautreau A, Scita G, Camonis J, Parrini MC. Direct interaction between exocyst and Wave complexes promotes cell protrusions and motility. J Cell Sci 2016; 129:3756-3769. [PMID: 27591259 DOI: 10.1242/jcs.187336] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/16/2016] [Indexed: 12/25/2022] Open
Abstract
Coordination between membrane trafficking and actin polymerization is fundamental in cell migration, but a dynamic view of the underlying molecular mechanisms is still missing. The Rac1 GTPase controls actin polymerization at protrusions by interacting with its effector, the Wave regulatory complex (WRC). The exocyst complex, which functions in polarized exocytosis, has been involved in the regulation of cell motility. Here, we show a physical and functional connection between exocyst and WRC. Purified components of exocyst and WRC directly associate in vitro, and interactions interfaces are identified. The exocyst-WRC interaction is confirmed in cells by co-immunoprecipitation and is shown to occur independently of the Arp2/3 complex. Disruption of the exocyst-WRC interaction leads to impaired migration. By using time-lapse microscopy coupled to image correlation analysis, we visualized the trafficking of the WRC towards the front of the cell in nascent protrusions. The exocyst is necessary for WRC recruitment at the leading edge and for resulting cell edge movements. This direct link between the exocyst and WRC provides a new mechanistic insight into the spatio-temporal regulation of cell migration.
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Affiliation(s)
- Marco Biondini
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France ART group, Inserm U830, Paris 75005, France
| | - Amel Sadou-Dubourgnoux
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France ART group, Inserm U830, Paris 75005, France
| | - Perrine Paul-Gilloteaux
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France Cell and Tissue Imaging Facility (PICT-IBiSA), CNRS UMR 144, Paris 75005, France
| | - Giulia Zago
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France ART group, Inserm U830, Paris 75005, France
| | - Melis D Arslanhan
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France ART group, Inserm U830, Paris 75005, France
| | - François Waharte
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France Cell and Tissue Imaging Facility (PICT-IBiSA), CNRS UMR 144, Paris 75005, France
| | | | - Maud Hertzog
- Laboratoire de Microbiologie et Génétique Moléculaire, CNRS UMR 5100, Université Paul Sabatier, Toulouse 31062, France
| | - Jinchao Yu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette 91191
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, Gif-sur-Yvette 91191
| | - Alexis Gautreau
- Laboratoire de Biochimie Ecole Polytechnique, CNRS UMR7654, Palaiseau Cedex 91128, France
| | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan 20139, Italy
| | - Jacques Camonis
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France ART group, Inserm U830, Paris 75005, France
| | - Maria Carla Parrini
- Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris 75005, France ART group, Inserm U830, Paris 75005, France
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18
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Yu J, Picord G, Tuffery P, Guerois R. HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. Bioinformatics 2015; 31:3850-2. [PMID: 26231431 DOI: 10.1093/bioinformatics/btv441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/21/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The HHsearch algorithm, implementing a hidden Markov model (HMM)-HMM alignment method, has shown excellent alignment performance in the so-called twilight zone (target-template sequence identity with ∼20%). However, an optimal alignment by HHsearch may contain small to large errors, leading to poor structure prediction if these errors are located in important structural elements. RESULTS HHalign-Kbest server runs a full pipeline, from the generation of suboptimal HMM-HMM alignments to the evaluation of the best structural models. In the HHsearch framework, it implements a novel algorithm capable of generating k-best HMM-HMM suboptimal alignments rather than only the optimal one. For large proteins, a directed acyclic graph-based implementation reduces drastically the memory usage. Improved alignments were systematically generated among the top k suboptimal alignments. To recognize them, corresponding structural models were systematically generated and evaluated with Qmean score. The method was benchmarked over 420 targets from the SCOP30 database. In the range of HHsearch probability of 20-99%, average quality of the models (TM-score) raised by 4.1-16.3% and 8.0-21.0% considering the top 1 and top 10 best models, respectively. AVAILABILITY AND IMPLEMENTATION http://bioserv.rpbs.univ-paris-diderot.fr/services/HHalign-Kbest/ (source code and server). CONTACT guerois@cea.fr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jinchao Yu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette
| | - Geraldine Picord
- INSERM U973, MTi, F-75205 Paris, Université Paris Diderot, Sorbonne Paris Cité F-75205 Paris and Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France
| | - Pierre Tuffery
- INSERM U973, MTi, F-75205 Paris, Université Paris Diderot, Sorbonne Paris Cité F-75205 Paris and Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette
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19
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Wang W, Shen T, Guerois R, Zhang F, Kuerban H, Lv Y, Gigant B, Knossow M, Wang C. New Insights into the Coupling between Microtubule Depolymerization and ATP Hydrolysis by Kinesin-13 Protein Kif2C. J Biol Chem 2015; 290:18721-31. [PMID: 26055718 DOI: 10.1074/jbc.m115.646919] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Indexed: 11/06/2022] Open
Abstract
Kinesin-13 proteins depolymerize microtubules in an ATP hydrolysis-dependent manner. The coupling between these two activities remains unclear. Here, we first studied the role of the kinesin-13 subfamily-specific loop 2 and of the KVD motif at the tip of this loop. Shortening the loop, the lysine/glutamate interchange and the additional Val to Ser substitution all led to Kif2C mutants with decreased microtubule-stimulated ATPase and impaired depolymerization capability. We rationalized these results based on a structural model of the Kif2C-ATP-tubulin complex derived from the recently determined structures of kinesin-1 bound to tubulin. In this model, upon microtubule binding Kif2C undergoes a conformational change governed in part by the interaction of the KVD motif with the tubulin interdimer interface. Second, we mutated to an alanine the conserved glutamate residue of the switch 2 nucleotide binding motif. This mutation blocks motile kinesins in a post-conformational change state and inhibits ATP hydrolysis. This Kif2C mutant still depolymerized microtubules and yielded complexes of one Kif2C with two tubulin heterodimers. These results demonstrate that the structural change of Kif2C-ATP upon binding to microtubule ends is sufficient for tubulin release, whereas ATP hydrolysis is not required. Overall, our data suggest that the conformation reached by kinesin-13s upon tubulin binding is similar to that of tubulin-bound, ATP-bound, motile kinesins but that this conformation is adapted to microtubule depolymerization.
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Affiliation(s)
- Weiyi Wang
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China, the Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette 91198, France, and
| | - Ting Shen
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China
| | - Raphael Guerois
- the Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette 91198, France, and the From CEA, Institut de Biologie et de la Technologies de Saclay (iBiTecS), Gif-sur-Yvette 91191, France
| | - Fuming Zhang
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China
| | - Hureshitanmu Kuerban
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China
| | - Yuncong Lv
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China
| | - Benoît Gigant
- the Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette 91198, France, and
| | - Marcel Knossow
- the Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette 91198, France, and
| | - Chunguang Wang
- From the Institute of Protein Research, Tongji University, Shanghai 200092, China,
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20
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Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail M, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Res 2015; 43:1905-17. [PMID: 25618846 PMCID: PMC4330383 DOI: 10.1093/nar/gkv021] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.
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Affiliation(s)
- Nicolas Richet
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Danni Liu
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | | | - Christophe Velours
- Laboratoire d'Enzymologie et de Biologie Structurale, CNRS UPR 3082, 1 avenue de la Terrasse, Gif-sur-Yvette, F-91190, France
| | - Armelle Corpet
- Institut Curie, Centre de Recherche, CNRS UMR 3664, Equipe Labellisée Ligue contre le Cancer, and Université Pierre et Marie Curie, Université Sorbonne PSL*, Paris, F-75248, France
| | - Albane Gaubert
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - May Bakail
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Gwenaelle Moal-Raisin
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Raphael Guerois
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Christel Compper
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Arthur Besle
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Berengère Guichard
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Genevieve Almouzni
- Institut Curie, Centre de Recherche, CNRS UMR 3664, Equipe Labellisée Ligue contre le Cancer, and Université Pierre et Marie Curie, Université Sorbonne PSL*, Paris, F-75248, France
| | - Françoise Ochsenbein
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
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21
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Wagner S, Stuttmann J, Rietz S, Guerois R, Brunstein E, Bautor J, Niefind K, Parker JE. Structural basis for signaling by exclusive EDS1 heteromeric complexes with SAG101 or PAD4 in plant innate immunity. Cell Host Microbe 2014; 14:619-30. [PMID: 24331460 DOI: 10.1016/j.chom.2013.11.006] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/02/2013] [Accepted: 11/11/2013] [Indexed: 11/15/2022]
Abstract
Biotrophic plant pathogens encounter a postinfection basal resistance layer controlled by the lipase-like protein enhanced disease susceptibility 1 (EDS1) and its sequence-related interaction partners, senescence-associated gene 101 (SAG101) and phytoalexin deficient 4 (PAD4). Maintainance of separate EDS1 family member clades through angiosperm evolution suggests distinct functional attributes. We report the Arabidopsis EDS1-SAG101 heterodimer crystal structure with juxtaposed N-terminal α/β hydrolase and C-terminal α-helical EP domains aligned via a large conserved interface. Mutational analysis of the EDS1-SAG101 heterodimer and a derived EDS1-PAD4 structural model shows that EDS1 signals within mutually exclusive heterocomplexes. Although there is evolutionary conservation of α/β hydrolase topology in all three proteins, a noncatalytic resistance mechanism is indicated. Instead, the respective N-terminal domains appear to facilitate binding of the essential EP domains to create novel interaction surfaces on the heterodimer. Transitions between distinct functional EDS1 heterodimers might explain the central importance and versatility of this regulatory node in plant immunity.
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Affiliation(s)
- Stephan Wagner
- University of Cologne, Department of Chemistry, Institute of Biochemistry, Otto-Fischer-Strß 12-14, 50674 Köln, Germany
| | - Johannes Stuttmann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany; Department of Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany
| | - Steffen Rietz
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Raphael Guerois
- CEA, Commissariat à l'Energie Atomique, iBiTecS, 91191 Gif-sur-Yvette, France; CNRS, 91191 Gif-sur-Yvette, France; University Paris-Sud, 91405 Orsay, France
| | - Elena Brunstein
- University of Cologne, Department of Chemistry, Institute of Biochemistry, Otto-Fischer-Strß 12-14, 50674 Köln, Germany
| | - Jaqueline Bautor
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Karsten Niefind
- University of Cologne, Department of Chemistry, Institute of Biochemistry, Otto-Fischer-Strß 12-14, 50674 Köln, Germany.
| | - Jane E Parker
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany.
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22
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Andreani J, Guerois R. Evolution of protein interactions: From interactomes to interfaces. Arch Biochem Biophys 2014; 554:65-75. [DOI: 10.1016/j.abb.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/28/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
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23
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Andreani J, Faure G, Guerois R. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. ACTA ACUST UNITED AC 2013; 29:1742-9. [PMID: 23652426 DOI: 10.1093/bioinformatics/btt260] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION Structural prediction of protein interactions currently remains a challenging but fundamental goal. In particular, progress in scoring functions is critical for the efficient discrimination of near-native interfaces among large sets of decoys. Many functions have been developed using knowledge-based potentials, but few make use of multi-body interactions or evolutionary information, although multi-residue interactions are crucial for protein-protein binding and protein interfaces undergo significant selection pressure to maintain their interactions. RESULTS This article presents InterEvScore, a novel scoring function using a coarse-grained statistical potential including two- and three-body interactions, which provides each residue with the opportunity to contribute in its most favorable local structural environment. Combination of this potential with evolutionary information considerably improves scoring results on the 54 test cases from the widely used protein docking benchmark for which evolutionary information can be collected. We analyze how our way to include evolutionary information gradually increases the discriminative power of InterEvScore. Comparison with several previously published scoring functions (ZDOCK, ZRANK and SPIDER) shows the significant progress brought by InterEvScore. AVAILABILITY http://biodev.cea.fr/interevol/interevscore CONTACT guerois@cea.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jessica Andreani
- CEA, iBiTecS, Service de Bioenergetique Biologie Structurale et Mecanismes SB2SM, Laboratoire de Biologie Structurale et Radiobiologie LBSR, F-91191 Gif sur Yvette, France
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24
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Stuttmann J, Hubberten HM, Rietz S, Kaur J, Muskett P, Guerois R, Bednarek P, Hoefgen R, Parker JE. Perturbation of Arabidopsis amino acid metabolism causes incompatibility with the adapted biotrophic pathogen Hyaloperonospora arabidopsidis. Plant Cell 2011; 23:2788-803. [PMID: 21784950 PMCID: PMC3226217 DOI: 10.1105/tpc.111.087684] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/27/2011] [Accepted: 07/07/2011] [Indexed: 05/18/2023]
Abstract
Reliance of biotrophic pathogens on living plant tissues to propagate implies strong interdependence between host metabolism and nutrient uptake by the pathogen. However, factors determining host suitability and establishment of infection are largely unknown. We describe a loss-of-inhibition allele of ASPARTATE KINASE2 and a loss-of-function allele of DIHYDRODIPICOLINATE SYNTHASE2 identified in a screen for Arabidopsis thaliana mutants with increased resistance to the obligate biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa). Through different molecular mechanisms, these mutations perturb amino acid homeostasis leading to overaccumulation of the Asp-derived amino acids Met, Thr, and Ile. Although detrimental for the plant, the mutations do not cause defense activation, and both mutants retain full susceptibility to the adapted obligate biotrophic fungus Golovinomyces orontii (Go). Chemical treatments mimicking the mutants' metabolic state identified Thr as the amino acid suppressing Hpa but not Go colonization. We conclude that perturbations in amino acid homeostasis render the mutant plants unsuitable as an infection substrate for Hpa. This may be explained by deployment of the same amino acid biosynthetic pathways by oomycetes and plants. Our data show that the plant host metabolic state can, in specific ways, influence the ability of adapted biotrophic strains to cause disease.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | | | - Steffen Rietz
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Jagreet Kaur
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Muskett
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Raphael Guerois
- Commissariat á l’Energie Atomique, Institut de Biologie et Technologies de Saclay, Laboratoire de Biologie Structurale et Radiobiologie and Centre National de la Recherche Scientifique, Unités de Recherche Associées 2096, F-91191 Gif-sur-Yvette, France
| | - Paweł Bednarek
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Address correspondence to
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Malivert L, Ropars V, Nunez M, Drevet P, Miron S, Faure G, Guerois R, Mornon JP, Revy P, Charbonnier JB, Callebaut I, de Villartay JP. Delineation of the Xrcc4-interacting region in the globular head domain of cernunnos/XLF. J Biol Chem 2010; 285:26475-83. [PMID: 20558749 DOI: 10.1074/jbc.m110.138156] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In mammals, the majority of DNA double-strand breaks are processed by the nonhomologous end-joining (NHEJ) pathway, composed of seven factors: Ku70, Ku80, DNA-PKcs, Artemis, Xrcc4 (X4), DNA-ligase IV (L4), and Cernunnos/XLF. Cernunnos is part of the ligation complex, constituted by X4 and L4. To improve our knowledge on the structure and function of Cernunnos, we performed a systematic mutagenesis study on positions selected from an analysis of the recent three-dimensional structures of this factor. Ten of 27 screened mutants were nonfunctional in several DNA repair assays. Outside amino acids critical for the expression and stability of Cernunnos, we identified three amino acids (Arg(64), Leu(65), and Leu(115)) essential for the interaction with X4 and the proper function of Cernunnos. Docking the crystal structures of the two factors further validated this probable interaction surface of Cernunnos with X4.
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Affiliation(s)
- Laurent Malivert
- INSERM, Hôpital Necker-Enfants Malades U768, Unité de Développement Normal et Pathologique du Système Immunitaire, Paris, France
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26
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Cariou B, Ouguerram K, Zaïr Y, Guerois R, Langhi C, Kourimate S, Benoit I, Le May C, Gayet C, Belabbas K, Dufernez F, Chétiveaux M, Tarugi P, Krempf M, Benlian P, Costet P. PCSK9 dominant negative mutant results in increased LDL catabolic rate and familial hypobetalipoproteinemia. Arterioscler Thromb Vasc Biol 2009; 29:2191-7. [PMID: 19762784 DOI: 10.1161/atvbaha.109.194191] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a central player in the regulation of cholesterol homeostasis, increasing the low-density lipoprotein (LDL) receptor degradation. Our study aimed at exploring the pathogenic consequences in vivo and in vitro of a PCSK9 prodomain mutation found in a family with hypobetalipoproteinemia (FHBL). METHODS AND RESULTS A white 49-year-old diabetic man had profound FBHL (LDLC: 16 mg/dL) whereas his daughter and sister displayed a milder phenotype (LDLC 44 mg/dL and 57 mg/dL, respectively), all otherwise healthy with a normal liver function. A monoallelic PCSK9 double-mutant R104C/V114A cosegregated with FBHL, with no mutation found at other FHBL-causing loci. A dose-effect was also found in FBHL relatives for plasma APOB and PCSK9 (very-low to undetectable in proband, approximately 50% decreased in sister and daughter) and LDL catabolic rate (256% and 88% increased in proband and daughter). Transient transfection in hepatocytes showed severely impaired processing and secretion of the double mutant which acted as a dominant negative over secretion of wild-type PCSK9. CONCLUSIONS These results show that heterozygous PCSK9 missense mutations may associate with profound hypobetalipoproteinemia and constitute the first direct evidence in human that decrease of plasma LDLC concentrations associated to PCSK9 LOF mutations are attributable to an increased clearance rate of LDL.
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27
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Abstract
This chapter focuses on the methods developed for the automatic or semiautomatic design of protein structures. We present several algorithms for the exploration of the sequence space and scoring of the designed models. There are now several successful designs that have been achieved using these approaches such as the stabilization of a protein fold, the stabilization of a protein-protein complex interface, and the optimization of a protein function. A rapid presentation of the methodologies is followed by a detailed analysis of two test case studies. The first one deals with the redesign of a protein hydrophobic core and the second one with the stabilization of a protein structure through mutations at the surface. The different approaches are compared and the consistency of the predictions with the experimental data are discussed. All the programs tested in these protocols are freely available through the internet and may be applied to a wide range of design issues.
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Affiliation(s)
- Hocine Madaoui
- Département de Biologie Joliot-Curie, CEA Saclay, Gif-sur-Yvette, France
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28
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Abstract
The progress achieved by several groups in the field of computational protein design shows that successful design methods include two major features: efficient algorithms to deal with the combinatorial exploration of sequence space and optimal energy functions to rank sequences according to their fitness for the given fold.
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Affiliation(s)
- Joaquim Mendes
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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29
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Abstract
We have developed a computer algorithm, FOLDEF (for FOLD-X energy function), to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of FOLDEF was tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins. FOLDEF uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FOLDEF have been weighted using empirical data obtained from protein engineering experiments. First, we considered a training database of 339 mutants in nine different proteins and optimised the set of parameters and weighting factors that best accounted for the changes in stability of the mutants. The predictive power of the method was then tested using a blind test mutant database of 667 mutants, as well as a database of 82 protein-protein complex mutants. The global correlation obtained for 95 % of the entire mutant database (1030 mutants) is 0.83 with a standard deviation of 0.81 kcal mol(-1) and a slope of 0.76. The present energy function uses a minimum of computational resources and can therefore easily be used in protein design algorithms, and in the field of protein structure and folding pathways prediction where one requires a fast and accurate energy function. FOLDEF is available via a web-interface at http://fold-x.embl-heidelberg.de
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30
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Abstract
The basic rules governing the folding of small, single-domain proteins are being discovered. New algorithms that can predict the major features of the folding process give the opportunity to design and optimise protein folding in a rational way. Recent experimental works suggest that sequence-specific features should be integrated in folding models to improve their performance.
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Affiliation(s)
- R Guerois
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany.
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31
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Ochsenbein F, Guerois R, Neumann JM, Sanson A, Guittet E, van Heijenoort C. 15N NMR relaxation as a probe for helical intrinsic propensity: the case of the unfolded D2 domain of annexin I. J Biomol NMR 2001; 19:3-18. [PMID: 11246852 DOI: 10.1023/a:1008390606077] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The isolated D2 domain of annexin I is unable to adopt a tertiary fold but exhibits both native and non-native residual structures. It thus constitutes an attractive model for the investigation of dynamics of partially folded states in the context of protein folding and stability. 15N relaxation parameters of the D2 domain have been acquired at three different magnetic fields, 500, 600 and 800 MHz. This enables the estimation of the contribution of conformational exchange to the relaxation parameters on the micro- to millisecond time scale, thus providing a suitable data set for the description of motions on the pico- and nanosecond time scale. The analysis of the seven spectral densities obtained (J(0), J(50 MHz), J(60 MHz), J(80 MHz), <J(500 MHz)>, <J(600 MHz)>, <J(800 MHz)>) provides complementary and meaningful results on the conformational features of the D2 domain structure previously depicted by chemical shift and NOE data. Especially, residual helix segments exhibit distinct dynamical behaviors that are related to their intrinsic helical propensity. Beside the spectral density analysis, a series of models derived from the Lipari and Szabo model-free approach are investigated. Two models containing three parameters are able to reproduce equally well the experimental data within experimental errors but provide different values of order parameters and correlation times. The inability to find a unique model to describe the data emphasizes the difficulty to use and interpret the model-free parameters in the case of partially or fully unfolded proteins consisting of a wide range of interconverting conformers.
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Affiliation(s)
- F Ochsenbein
- CNRS, Institut de Chimie des Substances Naturelles, Gif sur Yvette, France
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32
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Abstract
To investigate the relationships between protein topology, amino acid sequence and folding mechanisms, the folding transition state of the Sso7d protein has been characterised both experimentally and theoretically. Although Sso7d protein has a similar topology to that of the SH3 domains, the structure of its transition state is different from that of alpha-spectrin and src SH3 domains previously studied. The folding algorithm, Fold-X, including an energy function with specific sequence features, accounts for these differences and reproduces with a good agreement the set of experimental phi(double dagger-U) values obtained for the three proteins. Our analysis shows that taking into account sequence features underlying protein topology is critical for an accurate prediction of the folding process.
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Affiliation(s)
- R Guerois
- EMBL, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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33
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Beswick V, Guerois R, Cordier-Ochsenbein F, Coïc YM, Tam HD, Tostain J, Noël JP, Sanson A, Neumann JM. Dodecylphosphocholine micelles as a membrane-like environment: new results from NMR relaxation and paramagnetic relaxation enhancement analysis. Eur Biophys J 1999; 28:48-58. [PMID: 9933923 DOI: 10.1007/s002490050182] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To further examine to what extent a dodecyl-phosphocholine (DPC) micelle mimics a phosphatidylcholine bilayer environment, we performed 13C, 2H, and 31P NMR relaxation measurements. Our data show that the dynamic behavior of DPC phosphocholine groups at low temperature (12 degrees C) corresponds to that of a phosphatidylcholine interface at high temperature (51 degrees C). In the presence of helical peptides, a PMP1 fragment, or an annexin fragment, the DPC local dynamics are not affected whereas the DPC aggregation number is increased to match an appropriate area/volume ratio for accommodating the bound peptides. We also show that quantitative measurements of paramagnetic relaxation enhancements induced by small amounts of spin-labeled phospholipids on peptide proton signals provide a meaningful insight on the location of both PMP1 and annexin fragments in DPC micelles. The paramagnetic contributions to the relaxation were extracted from intra-residue cross-peaks of NOESY spectra for both peptides. The location of each peptide in the micelles was found consistent with the corresponding relaxation data. As illustrated by the study of the PMP1 fragment, paramagnetic relaxation data also allow us to supply the missing medium-range NOEs and therefore to complete a standard conformational analysis of peptides in micelles.
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Affiliation(s)
- V Beswick
- Département de Biologie Cellulaire et Moléculaire, URA CNRS 2096, Gif sur Yvette, France
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34
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Guerois R, Cordier-Ochsenbein F, Baleux F, Huynh-Dinh T, Neumann JM, Sanson A. A conformational equilibrium in a protein fragment caused by two consecutive capping boxes: 1H-, 13C-NMR, and mutational analysis. Protein Sci 1998; 7:1506-15. [PMID: 9684882 PMCID: PMC2144069 DOI: 10.1002/pro.5560070703] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The conformational properties of an 18 residues peptide spanning the entire sequence, L1KTPA5QFDAD10ELRAA15MKG, of the first helix (A-helix) of domain 2 of annexin I, were thoroughly investigated. This fragment exhibits several singular features, and in particular, two successive potential capping boxes, T3xxQ6 and D8xxE11. The former corresponds to the native hydrogen bond network stabilizing the alpha helix N-terminus in the protein; the latter is a non-native capping box able to break the helix at residue D8, and is observed in the domain 2 partially folded state. Using 2D-NMR techniques, we showed that two main populations of conformers coexist in aqueous solution. The first corresponds to a single helix extending from T3 to K17. The second corresponds to a broken helix at residue Ds. Four mutants, T3A, F7A, D8A, and E11A, were designed to further analyze the role of key amino acids in the equilibrium between the two ensembles of conformers. The sensitivity of NMR parameters to account for the variations in the populations of conformers was evaluated for each peptide. Our data show the delta13Calpha chemical shift to be the most relevant parameter. We used it to estimate the population ratio in the various peptides between the two main ensembles of conformers, the full helix and the broken helix. For the WT, E11A, and F7A peptides, these ratios are respectively 35/65, 60/40, 60/40. Our results were compared to the data obtained from helix/coil transition algorithms.
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Affiliation(s)
- R Guerois
- Département de Biologie Cellulaire et Moléculaire, URA CNRS 2096, CEA Saclay, Gif sur Yvette, France
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35
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Cordier-Ochsenbein F, Guerois R, Baleux F, Huynh-Dinh T, Lirsac PN, Russo-Marie F, Neumann JM, Sanson A. Exploring the folding pathways of annexin I, a multidomain protein. I. non-native structures stabilize the partially folded state of the isolated domain 2 of annexin I. J Mol Biol 1998; 279:1163-75. [PMID: 9642092 DOI: 10.1006/jmbi.1998.1829] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins of the annexin family constitute very attractive models because of their four approximately 70 residue domains, D1 to D4, exhibiting an identical topology comprising five helix segments with only a limited sequence homology of approximately 30%. We focus on the isolated D2 domain, which is only partially folded. A detailed analysis of this equilibrium partially folded state in aqueous solution and micellar solution using 15N-1H multidimensional NMR is presented. Comparison of the residual structure of the entire domain with that of shorter fragments indicates the presence of long-range transient hydrophobic interactions that slightly stabilize the secondary structure elements. The unfolded domain tends to behave as a four-helix, rather than as a five-helix domain. The ensemble of residual structures comprises: (i) a set of native structures consisting of three regions with large helix populations, in rather sharp correspondence with A, B and E helices, and a small helix population in the second part of the C helix; (ii) a set of non-native local structures corresponding to turn-like structures stabilized by several side-chain to side-chain interactions and helix-disruptive side-chains to backbone interactions. Remarkably, residues involved in these local non-native interactions are also involved, in the native structure, in structurally important non-local interactions. During the folding process of annexin I, the local non-native interactions have to switch to native long-range interactions. This structural switch reveals the existence of a sequence-encoded regulation of the folding pathways and kinetics, and emphasizes the key role of the non-native local structures in this regulation.
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Affiliation(s)
- F Cordier-Ochsenbein
- Département de Biologie Cellulaire et Moléculaire Section de Biophysique des Protéines et des Membranes and URA CNRS, 2096, Gif sur Yvette Cedex, France
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36
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Cordier-Ochsenbein F, Guerois R, Russo-Marie F, Neumann JM, Sanson A. Exploring the folding pathways of annexin I, a multidomain protein. II. Hierarchy in domain folding propensities may govern the folding process. J Mol Biol 1998; 279:1177-85. [PMID: 9642093 DOI: 10.1006/jmbi.1998.1828] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the context of exploring the relationship between sequence and folding pathways, the multi-domain proteins of the annexin family constitute very attractive models. They are constituted of four approximately 70-residue domains, named D1 to D4, with identical topologies but only limited sequence homology of approximately 30%. The domains are organized in a pseudochiral circular arrangement. Here, we report on the folding propensity of the D1 domain of annexin I obtained from overexpression in Escherichia coli. Unlike the D2 domain, which is only partially folded, the isolated D1 domain exhibits autonomous refolding in pure aqueous solution. Similarly, the D3 domain and D2-D3 module were obtained from expression in E. coli but were found to be largely unfolded. No conclusion could be drawn for the D4 domain because it was not possible to extract it from the bacterial inclusion bodies. The data allow us to propose a plausible scenario for the annexin I folding. This working model states that firstly the D1 domain folds, and the D2 and D3 domains remain partly unfolded, facilitating the docking of the D4 domain to the D1 domain. In a second step, the D1 and D4 domains dock, and D4 may fold if already not folded. The final step starts with the stabilization of the D1-D4 module. This stabilization is crucial for allowing the non-native local interactions inside the still partially unfolded D2 domain to switch to the native long-range interactions involving D4. This switch allows the complete folding of D2 and D3. The model proposes a sequential and hierarchical process for the folding of annexin I and emphasizes the role of both native framework and non-native structures in the process.
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Affiliation(s)
- F Cordier-Ochsenbein
- Section de Biophysique des Protéines et des Membranes and URA CNRS 2096, Gif sur Yvette Cedex, CEA Saclay, 91191, France
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37
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Cordier-Ochsenbein F, Guerois R, Baleux F, Huynh-Dinh T, Chaffotte A, Neumann JM, Sanson A. Folding properties of an annexin I domain: a 1H-15N NMR and CD study. Biochemistry 1996; 35:10347-57. [PMID: 8756690 DOI: 10.1021/bi960747v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The annexin fold consists of four 70-residue domains with markedly homologous sequences and nearly identical structures. Each domain contains five helices designated A to E. Domain 2 of annexin I was obtained by chemical synthesis including ten specifically labeled residues and studied by 1H-15N NMR and circular dichroism (CD). In pure aqueous solution this annexin domain presents, at most, 25% of residual helix secondary structure compared to 75%-85% for the native helix content and thus does not constitute an autonomous folding unit. Dodecylphosphocholine (DPC) micelles were used to provide the annexin domain with non-specific hydrophobic interactions. The structuring effect of micelles was thoroughly investigated by CD and 1H-15N NMR. Most, but not all, of the native helix secondary structure was recovered at DPC saturation. NMR data made it possible to determine the intrinsic helix propensity hierarchy of the different helix segments of the domain: A approximately B approximately E > C, D. This hierarchy is remarkably well correlated with the location of the helices in the native protein since A, B, and E helices are those in contact with the remaining parts of the protein. This result tends to support the view that, for large proteins like annexins (35 kDa), high intrinsic secondary structure propensities, at least helix propensity, in selected protein segments is necessary for a correct folding process. As a consequence this also indicates that important information concerning the folding pathway is encoded in the protein sequence.
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